Recycling

The materials used in technology level I are completely bio degradable. No problems here.
The materials used in technology level II stay around longer but naturally occur in nature.
In technology level III it gets problematic. Diamond doesn't really decay which is good for engineering but bad for nature.

Diamondoid Mechanosynthesis is an irreversible process. Once a DME is assembled it can not be taken apart again. The only way back to the biosphere is by burning. What will help alleviating this problem it the organisation of APM products into bigger microcomponents that can reversibly be joined together and thus can potentially be reused and recomposed.
More about microcomponents can be found in the section section Assembly Levels.

(speculativity warning!)

Sometime in the future there might be a global microcomponent redistribution system running through ouer streets into our houses leading to faucets where you can "tap" things from.
The microcomponents only need to run through the upper assembly levels of the nanofactory